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GenomeRIK / tama

Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
GNU General Public License v3.0
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TAMA GO: ORF and NMD predictions #92

Closed anchonggen closed 1 year ago

anchonggen commented 1 year ago

Hi, I would like to ask if TAMA GO: ORF and NMD predictions are available to predict lncRNAs.

Thanks, An

GenomeRIK commented 1 year ago

Hi An,

The TAMA ORF/NMD pipeline finds protein hits and CDS for the transcript models. If a transcript model has no hits this could be interpreted as possible a lncRNA. However, there are different ways of predicting lncRNA, so in general it is best to use a variety of methods to see what is consensus.

Thank you, Richard